[Chimera-users] hem group

[Elaine Meng]

Hi Tomas,
There is no reasonable way to do this using only Chimera. Here is one idea that includes Chimera but also text-editing PDB files:

(a) go to the PDB web site find another PDB that already has HEM in it, if possible a protein related to yours, and open that in Chimera too.  For example, your protein is open as model #0, and you open the other protein that includes a HEM residue as model #1.  RCSB PDB web site:
<http://www.rcsb.org/pdb/home/home.do>

(b) superimpose the two structures so that the HEM is in the place you want to put it in your protein.  Here is some discussion of different ways to superimpose structures in Chimera:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

(c) choose "File... Save PDB" from the Chimera menu and save model #1 as a PDB file "relative to" model #0. Be sure to save it somewhere you can find it for the next step.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>

(d) text-edit to create a new PDB file that has the HEM residue from the PDB file of model #1 that you just wrote, plus all the atoms (at least the atoms you want) from the original PDB file of model #0.

This would give a fairly crude model of your protein plus HEM. 
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco



On Feb 28, 2011, at 12:33 PM, ImRyLiBS9XN6ZXIgVGFt4XMi wrote:

> Hello,
> 
> I would like to add HAEM group to a protein reconstructed from pdb data. I
> am working on Windows platform.
> Could you please help me how can I do that?
> many thanks
> Tamas
> 
> 
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